Method to fabricate a nanochannel for dna sequencing based on narrow trench patterning process

ABSTRACT

Apparatus and methods relating to DNA sequencing are provided. In one embodiment, a DNA sequencing device includes a nanochannel having a width that is approximately 0.3 nm to approximately 20 nm. A pair of electrodes having portions exposed to the nanochannel may form a tunneling current electrode (TCE) with an electrode gap of approximately 0.1 nm to approximately 2 nm, and more particularly about 0.3 nm to about 1 nm. In one embodiment, at least one of the pair of electrodes is formed as a suspended electrode. An actuator may be associated with the suspended electrode to displace it relative to the other electrode. In various embodiments, the nanochannel and/or the electrodes may be formed using thermal reflow processes to reduce the size of such features.

RELATED APPLICATIONS

This application claims the benefit of the filing date of U.S.Provisional Application No. 62/453,307, filed on 1 Feb. 2017, andentitled METHOD TO FABRICATE A NANOCHANNEL FOR DNA SEQUENCING BASED ONNARROW TRENCH PATTERNING PROCESS, the disclosure of which isincorporated in its entirety by this reference.

SUMMARY

One aspect of the present disclosure relates to a DNA sequencing devicethat includes a substrate, an in-plane nanochannel positioned in thesubstrate, the nanochannel having a width in the range of about 0.3 nmto about 20 nm, and a pair of in-plane electrodes positioned in thesubstrate and arranged perpendicular to the nanochannel. Free ends ofthe electrodes are exposed in the nanochannel and spaced apart to forman electrode gap. The electrode gap is in the range of about 0.3 nm toabout 2 nm.

A height of the nanochannel may be in the range of about 5 nm to about20 nm. The electrodes may have a width in the range of about 0.1 nm toabout 20 nm. The electrodes may have a height in the range of about 5 nmto about 20 nm. The nanochannel may be formed in an insulator substrate.The nanochannel may include a metal layer positioned along a bottomsurface, and the metal layer may be covered with an insulator material.The insulator substrate may include SiO2 or glass.

At least one of the electrodes may be formed as a suspended electrode.An actuator may be associated with the suspended electrode andconfigured to laterally displace the electrode, altering the width ofthe electrode gap.

Another aspect of the present disclosure relates to a method of forminga nanochannel device for DNA sequencing. The method includes depositinga hard mask layer on an insulator substrate, depositing a first resistlayer on the hard mask layer, trench patterning the first resist layerto form a first trench, and shrinking the first trench using a thermalre-flow process. The method also include pattern transferring the firsttrench through the hard mask layer and into the insulator substrate,stripping the hard mask layer from the insulator substrate, filling thefirst trench with a fill material, trench patterning the insulatorsubstrate to form an electrode trench, the electrode trench intersectingthe first trench, depositing metal material in the electrode trench toform a pair of electrodes, and removing the fill material from the firsttrench to form a DNA nanochannel.

The method may include trench patterning using at least one of deepultraviolet (DUV) lithography, 193 nm lithography, e-beam lithography,and nanoimprint lithography (NIL). The method may include repeating thestep of shrinking the first trench until the first trench has a firsttrench width in the range of about 0.3 nm to about 20 nm. The patterntransferring may include reactive ion etching (RIE). The method mayinclude, after pattern transferring, stripping the first resist layerfrom the hard mask layer. The method may include, after stripping thehard mask layer, depositing a metal layer on the insulator substrate asa capping layer, the metal layer positioned along a bottom surface ofthe first trench, etching to remove the metal layer from the insulatorsubstrate except in the first trench, and depositing an insulatormaterial in the first trench to cover the metal layer.

Filling the first trench with the filler material may include spincoating the filler material on the insulator substrate and in the firsttrench, and etching back the filler material from the insulatorsubstrate except within the first trench. The method may include, afterfilling the first trench with the filler material, depositing a secondresist layer on the insulator substrate, trench patterning the secondresist layer to form a second trench, shrinking the second trench usingthe one or more thermal re-flow process, and trench patterning theinsulator substrate to form the electrode trench using the second trenchas a pattern.

The thermal re-flow process may include disposing a top coat over atleast a portion of the substrate and within the trench. The top coat mayinclude a water based solution with surfactants that have positively andnegatively charged functional groups. The device, with the top coat, isbaked for a prescribed time and at a prescribed temperature, and the topcoat is then remove. The device may then be rinsed with deionized water,the resulting trench width having shrunk in the process whilemaintaining the cross-sectional profile or geometry of the trench. Themethod may also include baking the device with the top coat at atemperature of approximately 100° C. to approximately 180° C. forapproximately 60 seconds to approximately 90 seconds, and removing thetop coat from the substrate and the first trench.

The method may include, after depositing metal material in the electrodetrench, etching back the metal material to expose the fill material. Themethod may include providing a base insulator layer on the substrate,wherein the first electrode layer is positioned on the base insulatorlayer. The electrodes may be spaced apart to form an electrode gap, theelectrode gap may be positioned in the nanochannel, and the electrodegap may have a width in the range of about 0.3 nm to about 1 nm. Themethod may include applying an electrical voltage to the electrodes tonarrow the electrode gap. A width of nanochannel may be in the range ofabout 0.3 nm to about 20 nm, and a height of the nanochannel may be inthe range of about 5 nm to about 20 nm. The electrode may have a widthin the range of about 0.1 nm to about 20 nm, and a height in the rangeof about 5 nm to about 20 nm.

Another aspect of the present disclosure relates to a method ofsequencing DNA. The method includes providing a DNA sequencing devicehaving a substrate, a nanochannel extending through a portion of thesubstrate, the nanochannel having a width in the range of about 0.3 nmto about 20 nm, and a pair of in-plane electrodes positioned in thesubstrate and arranged substantially perpendicular to the nanochannel, aportion of each electrode being exposed in the nanochannel to form anelectrode gap, the electrode gap being in the range of about 0.3 nm toabout 2 nm. The method further includes passing a DNA strand through theelectrode gap, detecting a change in electronic signal with theelectrodes as the DNA strand passes through the electrode gap, anddetermining a sequence of individual nucleotides of the DNA strand basedon the change in electronic signal.

The foregoing has outlined rather broadly the features and technicaladvantages of examples according to this disclosure so that thefollowing detailed description may be better understood. Additionalfeatures and advantages will be described below. The conception andspecific examples disclosed may be readily utilized as a basis formodifying or designing other structures for carrying out the samepurposes of the present disclosure. Such equivalent constructions do notdepart from the scope of the appended claims. Characteristics of theconcepts disclosed herein, including their organization and method ofoperation, together with associated advantages will be better understoodfrom the following description when considered in connection with theaccompanying figures. Each of the figures is provided for the purpose ofillustration and description only, and not as a definition of the limitsof the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

A further understanding of the nature and advantages of the presentdisclosure may be realized by reference to the following drawings. Inthe appended figures, similar components or features may have the samereference label. Further, various components of the same type may bedistinguished by following a first reference label with a dash and asecond label that may distinguish among the similar components. However,features discussed for various components, including those having a dashand a second reference label, apply to other similar components. If onlythe first reference label is used in the specification, the descriptionis applicable to any one of the similar components having the same firstreference label irrespective of the second reference label.

FIGS. 1A-1N illustrate fabrication steps for forming a DNA nanochanneldevice in accordance with an embodiment of the present disclosure.

FIGS. 2A-2D illustrate additional fabrication steps for forming a DNAnanochannel device in accordance with an embodiment of the presentdisclosure.

FIG. 3 shows an example shrink cycle using a thermal re-flow process inaccordance with the present disclosure.

FIG. 4 shows another example shrink cycle using a thermal re-flowprocess in accordance with the present disclosure.

FIG. 5 shows an electrode pair for use in a DNA nanochannel device inaccordance with the present disclosure.

FIG. 6 shows an example DNA nanochannel device in accordance with thepresent disclosure.

FIG. 7 shows the device of FIG. 4 with a sealing layer disposed atop theelectrodes and nanochannel.

FIG. 8 shows a diagram of a system in accordance with various aspects ofthis disclosure.

FIG. 9 is a flow diagram showing steps of an example method inaccordance with the present disclosure.

FIG. 10 is a flow diagram showing steps of another example method inaccordance with the present disclosure.

DETAILED DESCRIPTION

Despite considerable efforts, DNA sequencing today still suffers fromhigh costs and low speeds. To address all these issues, various methodshave been proposed over the past decade that would allow individual DNAstrands to be read directly. Among these, nanopore and nanochannel basedapproaches have emerged as the most promising. However, many challengesexist related to fabricating a channel and/or pore opening that issufficiently small to limit passage to a single DNA strand, and there isno such report of a relatively mature method that address this unmetneed.

Direct DNA sequencing has drawn attention due to its advantages on longread length, high throughput and low cost. Direct DNA sequencing methodsusing transverse tunneling current measurement have been studiedextensively in literature. However, a manufacturably viable direct DNAsequencing device with required dimensions for the gap between thenanoelectrodes, nor methods for creating such a device, have not beendiscovered. Conventional MEMS and nanofabrication methods are inadequatefor creating the required structure.

The present disclosure generally relates to DNA sequencing, and moreparticularly relates to DNA sequencing devices having nanochannels andnanoelectrodes, and related methods of fabricating such devices. Thepresent disclosure may also relate to DNA sequencing using such devices.

A method of fabricating a nanochannel in a DNA sequencing device withdimensions as small as a few nanometers is disclosed here. One featureof the device is the relative long, narrow nanochannel for guiding thesingle molecule DNA to flow through. Another feature of the device is atunneling current electrode (TCE) having a narrowing gap between theelectrode members of the TCE. The TCE gap is required to be as small as1 nm, or even smaller, in order to detect DNA signals at desired levels.The devices and methods disclosed herein may incorporate a two-stagenarrow trench patterning process and may include a step of rotation ofabout 90°. An advantage of using a trench patterning process instead ofan isolated line in the device provides the advantage of the trenchlimiting, if not avoiding, thin line pattern collapse issues associatedwith the formation of an isolated line.

A relatively fast and low-cost genome (DNA), transcriptome (RNA) andproteome (all proteins) sequencing method could lead to the developmentof personalized medicine (e.g., the ability to target drugs and medicaltreatments specially to an individual). However, fabrication of ananochannel for single molecular DNA sequencing is still a technicalchallenge due to the extremely small dimension involved with the devicesthat are used to conduct the sequencing. The devices and methodsdisclosed herein address at least some of these challenges.

As discussed above, the device and methods disclosed herein provide arelatively long and narrow channel for guiding the single molecule DNAto flow through the device, and an even narrower tunneling currentelectrode (TCE). The TCE gap is required to be as small as less thanabout 1 nm in order to detect the DNA signal at a desired level. Toreduce the TCE gap to less than about 1 nm, one TCE electrode member isformed as a suspended electrode, and a shear actuator is used at thiselectrode, as will be discussed in further detail below. In theproduction of the device, a thermal re-flow process may be used toproduce trenches with a reduced gap between adjacent vertical sidewalls.

FIGS. 1A-1N illustrate an example method of fabricating a nanochannelDNA sequencing device by depicting a series images shown in across-sectional perspective view, as the device is constructed throughvarious stages of fabrication. Referring to FIG. 1A, a first stepincludes deposition of a thin, hard mask (HM) layer 102 on an insulatorsubstrate 104. The substrate may comprise, for example, SiO2 or glass. Aresist layer 106 may, for example, be spin-coated on a top surface ofthe HM layer 102.

As seen in FIG. 1B, a second step includes patterning a trench 108 inthe resist layer 106. The trench 108 may be patterned using any of avarious lithography tools, including, for example, deep ultraviolet(DUV) lithography, 193 nm lithography, e-beam lithography, nanoimprintlithography (NIL), and so on. As shown in FIG. 1C, (and as will bediscussed in further detail below) the trench is shrunk and smoothedusing a thermal re-flow process wherein width of the trench isdecreased. This re-flowing process can be repeated until achieving atargeted narrow trench width, for example, in a range of about 10 nm toabout 20 nm. Thus, comparing FIGS. 1B and 1C, the trench width isdecreased from a width of “a”, as shown in FIG. 1B, to a width of “b” asindicated in FIG. 1C.

Referring to FIG. 1D, a pattern transfer into HM layer takes place andthen into the substrate using, for example reactive ion etching (RIE)creating a trench 110 in the insulator substrate 104. The HM layer 102is then stripped as shown in FIG. 1E, and a metal layer 112 is depositedas a capping layer over the substrate 104, including on the floor of thetrench 110 as shown in FIG. 1F. It is noted that the metal, or metalmaterials, in this description may generally refer to a conductor or anelectronically conductive material, and may include any desiredconductive material.

As seen in FIG. 1G, an etching back step is performed to remove themetal capping layer 112 from the upper surface of the substrate 104, butnot from inside the narrow trench. Next, as shown in FIG. 1H, a thininsulator material 114 is disposed within the trench 110, covering themetal layer 112 disposed on the floor of trench 110. A temporary fillmaterial 116 is deposited to fill the trench 110 as shown in FIG. 1I. Inone embodiment the deposition of the fill material may be effected byfirst spin coating the material across the entire device, filling thetrench, and then etching back the material to remove it from the uppersurface of the substrate 104 while leaving the material in the trench110. The fill material may include a material that is generallyresistant to etching by plasma oxygen processes, but may be removed by awet etch process or by a dry etch process using a gas other than oxygen.Examples of some materials that may be used as the fill material 116include, but are not limited to, Cr, Ti, SiN, and SiON.

A second trench, oriented at an angle (e.g., 90°) from the first trench110 is formed using trench patterning and thermal re-flow processes asillustrated in FIGS. 1J-1N. For example, a resist layer 120 is formedover the substrate 104 and a trench 122 may be patterned in the resistlayer 120 as indicated FIG. 1J. The trench 122 may be patterned usingany of a various lithography tools such as described above. While notspecifically shown, a re-flow process may be used to decrease the widthof the trench 122 formed in the resist layer 120 such as previouslynoted and as will be further detailed below.

The trench pattern is transferred into the substrate, as seen in FIG.1K, but the process does not etch the fill material 116, forming a newtrench 124 in the substrate which is at a desired angle (e.g., 90°)relative to the first trench 110. A metal material may then be depositedinto the trench 124 formed within the substrate 104, forming metal lines126 that will be use in a tunneling current electrode (TCE). Next theresist layer 120 is stripped, and the substrate 104 may be slightlyetched back such that the fill material 116 has an open line as shown inFIG. 1M. The fill material 116 is then removed, leaving the trench 110for use as a DNA nanochannel.

Referring to FIGS. 2A-2D, a thermal re-flow process, such as used informing trenches as described above, is illustrated. FIG. 2A shows across-sectional side view of a device including an HM layer 102 formedon a substrate 104, and a resist layer 106 disposed over the HM layer102, the resist layer having a trench 108 formed therein, such aspreviously described with respect to FIG. 1B. The trench 108 has aninitial width of dimension “a” as seen in FIG. 2A.

As illustrated in FIG. 2B, a top coat 130 of thermal re-flow material isformed over the resist layer 106 and into trench 108. In one embodiment,the top coat may include a water-based solution with surfactants thathave positively and negatively charged functional groups. The positivelyand negatively charged functional groups may interact with each otherindirectly through the water (or other easily polarized medium). Asindicated in FIG. 2C, the device is baked (for example, at approximately100-180° C. for approximately 90 seconds), evaporating the water fromthe top coat material, enabling the positively and negatively chargedfunctional groups to have direct interactions with each other. Thedirect interactions of the functional groups cause the top coat materialto maintain the profile of the resist material 106 (e.g., the profile ofthe trench 108) while the top coat material undergoes thermal expansion.This enables the sidewalls of the trench 108 formed in the resist layerto remain vertical in its previously determined pattern, while shrinkingthe width of the trench 108 by effectively moving the walls of thetrench closer to one another. The top coat 130 is removed, the resistmaterial 106 is rinsed with deionized water, and the resulting trench108 formed in the resist material 106 exhibits a width “b”, thedimension “b” being smaller than the dimension “a” as indicated in FIG.2D.

The thermal re-flow process may be repeated multiple times to furthershrink the width of the trench if desired. For example, FIGS. 3 and 4are microphotographs depicting a trench formed in a device that hasundergone multiple thermal re-flow processes such as described above. Asseen in FIG. 3, an first specimen 140 starts out with a trench width, ora gap, or 37 nm. After a first thermal re-flow process, or “shrinkcycle,” the gap is reduced to 22 nm. After a second shrink cycle, thegap is narrowed to 16 nm. A third shrink cycle caused the gap tocompletely close.

The second specimen 150 shown in FIG. 3 shows an initial gap of 50 nm, agap of 34 nm after a first shrink cycle, a gap of 22 nm after a secondshrink cycle, and a gap of 19 nm after a third shrink cycle.

The third specimen 160 shown in FIG. 3 shows an initial gap of 80 nm, agap of 60 nm after a first shrink cycle, a gap of 37 nm after a secondshrink cycle, and a gap of 22 nm after a third shrink cycle.

Referring to FIG. 4, a profile view of a specimen 170 is shown that hasbeen subjected to multiple shrink cycles or thermal re-flow processes.The specimen 170 shows an initial gap of 75 nm, a gap of 50 nm after afirst shrink cycle, a gap of 35 nm after a second shrink cycle, and agap of 22 nm after a third shrink cycle. It is noted that the sidewallsof the trench remain vertical, providing a trench or channel with a veryhigh aspect ratio (e.g., 1:20 or even greater).

In providing a DNA sequencing device, it may be desirable to provide aTCE electrode with a TCE gap of approximately 1 nm or less. In oneembodiment that provides such a small TCE gap, at least one of the TCEelectrode members may be configured as a suspended electrode. Forexample, as generally shown in FIG. 5, a TCE electrode 200 may include afirst electrode member 202 which may be a “fixed” member, and a secondelectrode member 204 which is configured as a suspended member and maybe laterally displaceable relative to the first electrode member 202 asindicated by directional arrow 206. For example, an actuator 208 may beused to reduce the TCE gap down to a value of less than 1 nm. Whileshown schematically in FIG. 5, such an actuator 208 may be integratedinto the resulting device (e.g., as an “on-chip” actuator), using knownnanofabrication techniques as will be appreciated by those of ordinaryskill in the art. The formation of a suspended electrode member may beaccomplished using techniques discussed above, by deposition of metalonto a suspended pre-defined line structure using known nanofabricationtechniques.

Referring to FIGS. 6 and 7, a DNA sequencing device 250 is shownaccording to one example of the present disclosure. FIG. 7 depicts thedevice 250 with a top seal 252 in place, while FIG. 6 depicts the devicewith the top seal removed for purposes of clarity. In one embodiment,the top seal 252 may include polydimethylsiloxane (PDMS). For example,the PDMS material may be mixed with a curing agent at a ratio of 10:1(by weight), applied to a mold and then baked in an oven atapproximately 150° C. for approximately 10 minutes. This produces arubber film which may be placed on the device (e.g., on a device such asshown in FIG. 1N). The device and rubber film are then both exposed toan oxygen plasma treatment for approximately 1-3 minutes to bond therubber film to the device and also causing the rubber film to becomesuper-hydrophilic.

Still referring to FIGS. 6 and 7, the device 250 includes an insulatingsubstrate 254 in which is formed a channel 256 through which a singlestrand of DNA may be passed. The channel may be constructed, forexample, similar to, and in accordance with, the devices and processesdescribed hereinabove. In one embodiment, the channel 256 may exhibit awidth (between its two sidewalls) of approximately 0.3 nm toapproximately 20 nm and, in one particular embodiment, approximately 10nm to approximately 20 nm. The channel 256 may also exhibit a height ofapproximately 5 nm to approximately 20 nm and, more particularly,approximately 10 nm to approximately 20 nm.

The device 250 further includes a TCE 200 (such as shown in FIG. 5)having a first electrode member 202 and a second electrode member 204.The first electrode member 202 includes a conductive line 260 extendingthrough a portion of the insulating substrate 254. Likewise, the secondelectrode member 204 includes a conductive line 262 extending through aportion of the insulating substrate 254. In one embodiment, theconductive lines 260 and 262 of the TCE 200 may exhibit a width ofapproximately 0.3 nm to approximately 20 nm, and more particularlyapproximately 10 nm to approximately 20 nm. Additionally, the conductivelines 260 and 262 may exhibit a height of approximately 5 nm toapproximately 20 nm and, more particularly, approximately 10 nm toapproximately 20 nm. The electrode members 202 and 204 may beconstructed, for example, similar to, and in accordance with, thedevices and processes described hereinabove.

The first and second electrode members 202 and 204 may each include arefined tip (e.g., pointed or exhibiting a desired radius) positioned ata desired distance relative to each other. In one embodiment, anactuator 208 may be associated with the second electrode member 204,which may be configured as a suspended electrode, such that it may bedisplaced relative to the first electrode member 202, changing the gapdistance between the two electrode members 202 and 204. In anotherembodiment, each of the electrode members 202 and 204 may be configuredas suspended electrodes and have actuators associated therewith suchthat each electrode member 202 and 204 is independently displaceablerelative to the other. In one embodiment, the TCE electrode isconfigured to exhibit a gap between the two electrode members 202 and204 (i.e., the “TCE gap” of approximately 0.1 nm to approximately 2 nm,and more particularly approximately 0.3 nm to approximately 1 nm.

The device 250 further includes a second pair of electrode members 272and 274 associated with the DNA channel 256. A first voltage 276 may beapplied across the second pair of electrode members 272 and 274 to actas a motive force in drawing a DNA strand through the channel 256 andpast the TCE electrode gap 280. A second voltage 278 may be applied tothe TCE electrode 200 to read the signal of a DNA strand as it passesthrough the TCE gap formed in the channel 256.

FIG. 8 shows a system 300 for use with the DNA sequencing devices andsystems shown in FIGS. 1-7. System 300 may include a control panel 365.Control panel 365 may be equivalent at least in part to a controller,control unit, processor or the like for use with the devices describedabove with reference to FIGS. 1-3. Control panel 365 may includesequencing module 345. The sequencing module 345 may providecommunications with one or more electrodes 360 (also referred to assensors or devices) directly or via other communication components, suchas a transceiver 330 and/or antenna 335. The electrodes 360 mayrepresent one or more of the electrodes 126, 206, or pairs of suchelectrodes in any of the embodiments described above. The sequencingmodule 345 may perform or control various operations associated with,for example, the electrodes 126, 206, actuator 208, controller, or othercomponents of the DNA sequencing devices and related systems asdescribed above with reference to FIGS. 1-7.

Control panel 365 may also include a processor module 305, and memory310 (including software/firmware code (SW) 315), an input/outputcontroller module 320, a user interface module 325, a transceiver module330, and one or more antennas 335 each of which may communicate,directly or indirectly, with one another (e.g., via one or more buses340). The transceiver module 330 may communicate bi-directionally, viathe one or more antennas 335, wired links, and/or wireless links, withone or more networks or remote devices. For example, the transceivermodule 330 may communicate bi-directionally with one or more of device350 and/or electrodes 360-a, 360-c. The device 350 may be components ofthe DNA sequencing devices and related systems and devices describedwith reference to FIGS. 1-7, or other devices in communication with suchsystems and devices. The transceiver 330 may include a modem to modulatethe packets and provide the modulated packets to the one or moreantennas 335 for transmission, and to demodulate packets received fromthe one or more antennas 335. In some embodiments (not shown) thetransceiver may be communicate bi-directionally with one or more ofdevice 350, remote control device 355, and/or electrodes 360-a, 360-cthrough a hardwired connection without necessarily using antenna 335.While a control panel or a control device (e.g., 305) may include asingle antenna 335, the control panel or the control device may alsohave multiple antennas 335 capable of concurrently transmitting orreceiving multiple wired and/or wireless transmissions. In someembodiments, one element of control panel 365 (e.g., one or moreantennas 335, transceiver module 330, etc.) may provide a connectionusing wireless techniques, including digital cellular telephoneconnection, Cellular Digital Packet Data (CDPD) connection, digitalsatellite data connection, and/or another connection.

The signals associated with system 300 may include wirelesscommunication signals such as radio frequency, electromagnetics, localarea network (LAN), wide area network (WAN), virtual private network(VPN), wireless network (using 302.11, for example), 345 MHz, Z-WAVE®,cellular network (using 3G and/or LTE, for example), and/or othersignals. The one or more antennas 335 and/or transceiver module 330 mayinclude or be related to, but are not limited to, WWAN (GSM, CDMA, andWCDMA), WLAN (including BLUETOOTH® and Wi-Fi), WMAN (WiMAX), antennasfor mobile communications, antennas for Wireless Personal Area Network(WPAN) applications (including RFID and UWB). In some embodiments, eachantenna 335 may receive signals or information specific and/or exclusiveto itself. In other embodiments, each antenna 335 may receive signals orinformation not specific or exclusive to itself.

In some embodiments, one or more electrodes 360 (e.g., voltage,inductance, resistance, current, force, temperature, etc.) or devices350 may connect to some element of system 300 via a network using one ormore wired and/or wireless connections. In some embodiments, the userinterface module 325 may include an audio device, such as an externalspeaker system, an external display device such as a display screen,and/or an input device (e.g., remote control device interfaced with theuser interface module 325 directly and/or through I/O controller module320).

One or more buses 340 may allow data communication between one or moreelements of control panel 365 (e.g., processor module 305, memory 310,I/O controller module 320, user interface module 325, etc.).

The memory 310 may include random access memory (RAM), read only memory(ROM), flash RAM, and/or other types. The memory 310 may storecomputer-readable, computer-executable software/firmware code 315including instructions that, when executed, cause the processor module305 to perform various functions described in this disclosure (e.g.,initiating an adjustment of a lighting system, etc.). Alternatively, thesoftware/firmware code 315 may not be directly executable by theprocessor module 305 but may cause a computer (e.g., when compiled andexecuted) to perform functions described herein. Alternatively, thecomputer-readable, computer-executable software/firmware code 315 maynot be directly executable by the processor module 305 but may beconfigured to cause a computer (e.g., when compiled and executed) toperform functions described herein. The processor module 305 may includean intelligent hardware device, e.g., a central processing unit (CPU), amicrocontroller, an application-specific integrated circuit (ASIC), etc.

In some embodiments, the memory 310 can contain, among other things, theBasic Input-Output system (BIOS) which may control basic hardware and/orsoftware operation such as the interaction with peripheral components ordevices. For example, the sequencing module 345, and other modules andoperational components of the control panel 365 used to implement thepresent systems and methods may be stored within the system memory 310.Applications resident with system 300 are generally stored on andaccessed via a non-transitory computer readable medium, such as a harddisk drive or other storage medium. Additionally, applications can be inthe form of electronic signals modulated in accordance with theapplication and data communication technology when accessed via anetwork interface (e.g., transceiver module 330, one or more antennas335, etc.).

Many other devices and/or subsystems may be connected to one or may beincluded as one or more elements of system 300. In some embodiments, allof the elements shown in FIG. 8 need not be present to practice thepresent systems and methods. The devices and subsystems can beinterconnected in different ways from that shown in FIG. 8. In someembodiments, an aspect of some operation of a system, such as that shownin FIG. 8, may be readily known in the art and are not discussed indetail in this application. Code to implement the present disclosure canbe stored in a non-transitory computer-readable medium such as one ormore of system memory 310 or other memory. The operating system providedon I/O controller module 320 may be iOS®, ANDROID®, MS-DOS®,MS-WINDOWS®, OS/2®, UNIX®, LINUX®, or another known operating system.

The transceiver module 330 may include a modem configured to modulatethe packets and provide the modulated packets to the antennas 335 fortransmission and/or to demodulate packets received from the antennas335. While the control panel or control device (e.g., 305) may include asingle antenna 335, the control panel or control device (e.g., 305) mayhave multiple antennas 335 capable of concurrently transmitting and/orreceiving multiple wireless transmissions.

FIGS. 9 and 10 are flow diagrams illustrating example methods associatedwith the DNA sequencing devices disclosed herein. FIG. 9 illustrates amethod 400 method of forming a nanochannel device for DNA sequencing. Atblock 405, the method 400 includes depositing a hard mask layer on aninsulator substrate. Block 410 includes depositing a first resist layeron the hard mask layer. Block 415 includes trench patterning the firstresist layer to form a first trench. Block 420 includes shrinking thefirst trench using a thermal re-flow process. Block 425 includes patterntransferring the first trench through the hard mask layer and into theinsulator substrate. Block 430 includes stripping the hard mask layerfrom the insulator substrate. Block 435 includes filling the firsttrench with a fill material. Block 440 includes trench patterning theinsulator substrate to form an electrode trench, the electrode trenchintersecting the first trench. Block 445 includes depositing metalmaterial in the electrode trench to form a pair of electrodes. Block 450includes removing the fill material from the first trench to form a DNAnanochannel.

The method 400 may also include trench patterning using at least one ofdeep ultraviolet (DUV) lithography, 193 nm lithography, e-beamlithography, and nanoimprint lithography (NIL). The method 400 mayinclude repeating the step of shrinking the first trench until the firsttrench has a first trench width in the range of about 0.3 nm to about 20nm. Shrinking the first trench using a thermal re-flow process mayinclude disposing a top coat over at least a portion of the substrateand within the first trench, baking the device with the top coat at atemperature of approximately 100° C. to approximately 180° C. forapproximately 60 seconds to approximately 90 seconds, and removing thetop coat from the substrate and the first trench. The method 400 mayinclude, after stripping the hard mask layer, depositing a metal layeron the insulator substrate as a capping layer, the metal layerpositioned along a bottom surface of the first trench, etching to removethe metal layer from the insulator substrate except in the first trench,and depositing an insulator material in the first trench to cover themetal layer deposited in the first trench. Filling the first trench withthe filler material may include spin coating the filler material on theinsulator substrate and in the first trench, and etching back the fillermaterial from the insulator substrate except within the first trench.

The method 400 may include, after filling the first trench with thefiller material, depositing a second resist layer on the insulatorsubstrate, trench patterning the second resist layer to form a secondtrench, shrinking the second trench using the thermal re-flow process,and trench patterning the insulator substrate to form the electrodetrench using the second trench as a pattern. The method 400 may include,after depositing metal material in the electrode trench, etching backthe metal material to expose the fill material. The electrodes may bespaced apart to form an electrode gap, the electrode gap positioned inthe nanochannel and exhibiting a width in the range of about 0.3 nm toabout 2 nm. The method 400 may include forming at least a firstelectrode of the electrode pair as a suspended electrode and couplingthe first electrode with an actuator to displace the first electroderelative to a second electrode of the electrode pair to vary the widthof the electrode gap. A width of nanochannel may be in the range ofabout 0.3 nm to about 20 nm, and a height of the nanochannel may be inthe range of about 5 nm to about 20 nm, and the electrode may have awidth in the range of about 0.1 nm to about 20 nm, and a height in therange of about 5 nm to about 20 nm.

FIG. 10 illustrates a method 500 of DNA sequencing. The method 500 mayinclude, at block 505, providing a DNA sequencing device having asubstrate, a nanochannel extending through a portion of the substrate,the nanochannel having a width in the range of about 0.3 nm to about 20nm, and a pair of in-plane electrodes positioned in the substrate andarranged substantially perpendicular to the nanochannel, a portion ofeach electrode being exposed in the nanochannel to form an electrodegap, the electrode gap being in the range of about 0.3 nm to about 2 nm.The method 500 further includes passing a DNA strand through theelectrode gap, detecting a change in electronic signal with theelectrodes as the DNA strand passes through the electrode gap, anddetermining a sequence of individual nucleotides of the DNA strand basedon the change in electronic signal.

The example methods 400, 500 may, in other embodiments, include fewer oradditional steps that those illustrated in FIGS. 9 and 10. Further, manyother methods and method steps may be possible based on the disclosuresprovided herein.

In some embodiments, the DNA sequencing device and systems describedherein may be used to collect electronic signals associated with thenucleotides of a DNA strand passing through the gap between electrodepairs, and the collected electronic signals are processed at a differentlocation. The processing may include electronically comparing thecollected electronic signals to ranges of electronic signals associatedwith specific nucleotide types which have been previously determined andstored. In other embodiments, the DNA sequencing device includescapability of processing the collected electronic signals, conductingsuch comparison evaluations, and even formulating an order or sequencefor the nucleotides of the DNA strand being evaluated.

INCORPORATION BY REFERENCE

The entire content of each of the previously filed provisional patentapplications listed below are incorporated by reference in theirentireties into this document, as are the related non-provisional patentapplications of the same title filed concurrently with the presentapplication. If the same term is used in both this document and one ormore of the incorporated documents, then it should be interpreted tohave the broadest meaning imparted by any one or combination of thesesources unless the term has been explicitly defined to have a differentmeaning in this document. If there is an inconsistency between any ofthe following documents and this document, then this document shallgovern. The incorporated subject matter should not be used to limit ornarrow the scope of the explicitly recited or depicted subject matter.

-   -   U.S. Prov. App. No. 62/453,270, titled “SINGLE-MOLECULE DNA        SEQUENCING METHOD USING CONFINED NANO-FLUIDIC CHANNEL AND        SUB-NANOMETER ELECTRODE GAP,” filed on 1 Feb. 2017, and U.S.        patent application Ser. No. ______, titled “SINGLE-MOLECULE DNA        SEQUENCING METHOD USING CONFINED NANO-FLUIDIC CHANNEL AND        SUB-NANOMETER ELECTRODE GAP,” filed on 1 Feb. 2018.    -   U.S. Prov. App. No. 62/453,398, titled “NANOFLUIDIC CHANNEL        OPENING SIZE CONTROL USING ACTUATION,” filed on 1 Feb. 2017, and        U.S. patent application Ser. No. ______, titled “NANOFLUIDIC        CHANNEL OPENING SIZE CONTROL USING ACTUATION,” filed on 1 Feb.        2018.    -   U.S. Prov. App. No. 62/453,298, titled “FABRICATION OF        NANOCHANNEL WITH INTEGRATED ELECTRODES FOR DNA SEQUENCING USING        TUNNELING CURRENT,” filed on 1 Feb. 2017, and U.S. patent        application Ser. No. ______, titled “FABRICATION OF NANOCHANNEL        WITH INTEGRATED ELECTRODES FOR DNA SEQUENCING USING TUNNELING        CURRENT,” filed on 1 Feb. 2018.    -   U.S. Prov. App. No. 62/453,323, titled “FABRICATION OF A DEVICE        FOR SINGLE-MOLECULE DNA SEQUENCING USING SIDEWALL LITHOGRAPHY,”        filed on 1 Feb. 2017, and U.S. patent application Ser. No.        ______, titled “FABRICATION OF A DEVICE FOR SINGLE-MOLECULE DNA        SEQUENCING USING SIDEWALL LITHOGRAPHY,” filed on 1 Feb. 2018.    -   U.S. Prov. App. No. 62/453,339, titled “FABRICATION OF A        NANOCHANNEL FOR DNA SEQUENCING USING ELECTRICAL PLATING TO        ACHIEVE TUNNELING ELECTRODE GAP,” filed on 1 Feb. 2017, and U.S.        patent application Ser. No. ______, titled “FABRICATION OF A        NANOCHANNEL FOR DNA SEQUENCING USING ELECTRICAL PLATING TO        ACHIEVE TUNNELING ELECTRODE GAP,” filed on 1 Feb. 2018.    -   U.S. Prov. App. No. 62/453,346, titled “NANOSTRUCTURES TO        CONTROL DNA STRAND ORIENTATION AND POSITION LOCATION FOR        TRANSVERSE DNA SEQUENCING,” filed on 1 Feb. 2017, and U.S.        patent application Ser. No. ______, titled “NANOSTRUCTURES TO        CONTROL DNA STRAND ORIENTATION AND POSITION LOCATION FOR        TRANSVERSE DNA SEQUENCING,” filed on 1 Feb. 2018.    -   U.S. Prov. App. No. 62/453,365, titled “FABRICATION OF WEDGE        SHAPED ELECTRODE FOR ENHANCED DNA SEQUENCING USING TUNNELING        CURRENT,” filed on 1 Feb. 2017, and U.S. patent application Ser.        No. ______, titled “FABRICATION OF WEDGE SHAPED ELECTRODE FOR        ENHANCED DNA SEQUENCING USING TUNNELING CURRENT,” filed on 1        Feb. 2018.    -   U.S. Prov. App. No. 62/453,329, titled “DIRECT SEQUENCING DEVICE        WITH A TOP-BOTTOM ELECTRODE PAIR,” filed on 1 Feb. 2017, and        U.S. patent application Ser. No. ______, titled “DIRECT        SEQUENCING DEVICE WITH A TOP-BOTTOM ELECTRODE PAIR,” filed on 1        Feb. 2018.    -   U.S. Prov. App. No. 62/453,376, titled “MICRO AND NANOFLUIDIC        CHANNEL CONTROLLED ACTUATION TO OPEN CHANNEL GAP,” filed on 1        Feb. 2017.    -   U.S. Prov. App. No. 62/469,393, titled “METHOD TO AMPLIFY        TRANSVERSE TUNNELING CURRENT DISCRIMINATION OF DNA NUCLEOTIDES        VIA NUCLEOTIDE SITE SPECIFIC ATTACHMENT OF DYE-PEPTIDE,” filed        on 9 Mar. 2017, and U.S. patent application Ser. No. ______,        titled “METHOD TO AMPLIFY TRANSVERSE TUNNELING CURRENT        DISCRIMINATION OF DNA NUCLEOTIDES VIA NUCLEOTIDE SITE SPECIFIC        ATTACHMENT OF DYE-PEPTIDE,” filed on 9 Mar. 2018.    -   U.S. Prov. App. No. 62/469,409, titled “VERTICAL NANOPORE        COUPLED WITH A PAIR OF TRANSVERSE ELECTRODES HAVING A UNIFORM        ULTRASMALL NANOGAP FOR DNA SEQUENCING,” filed on 9 Mar. 2017,        and U.S. patent application Ser. No. ______, titled “VERTICAL        NANOPORE COUPLED WITH A PAIR OF TRANSVERSE ELECTRODES HAVING A        UNIFORM ULTRASMALL NANOGAP FOR DNA SEQUENCING,” filed on 9 Mar.        2018.

The detailed description set forth above in connection with the appendeddrawings describes examples and does not represent the only instancesthat may be implemented or that are within the scope of the claims. Theterms “example” and “exemplary,” when used in this description, mean“serving as an example, instance, or illustration,” and not “preferred”or “advantageous over other examples.” The detailed description includesspecific details for the purpose of providing an understanding of thedescribed techniques. These techniques, however, may be practicedwithout these specific details. In some instances, known structures andapparatuses are shown in block diagram form in order to avoid obscuringthe concepts of the described examples.

In addition, any disclosure of components contained within othercomponents or separate from other components should be consideredexemplary because multiple other architectures may potentially beimplemented to achieve the same functionality, including incorporatingall, most, and/or some elements as part of one or more unitarystructures and/or separate structures.

The previous description of the disclosure is provided to enable aperson skilled in the art to make or use the disclosure. Variousmodifications to the disclosure will be readily apparent to thoseskilled in the art, and the generic principles defined herein may beapplied to other variations without departing from the scope of thedisclosure. Thus, the disclosure is not to be limited to the examplesand designs described herein but is to be accorded the broadest scopeconsistent with the principles and novel features disclosed.

The process parameters, actions, and steps described and/or illustratedin this disclosure are given by way of example only and can be varied asdesired. For example, while the steps illustrated and/or described maybe shown or discussed in a particular order, these steps do notnecessarily need to be performed in the order illustrated or discussed.The various exemplary methods described and/or illustrated here may alsoomit one or more of the steps described or illustrated here or includeadditional steps in addition to those disclosed.

This description, for purposes of explanation, has been described withreference to specific embodiments. The illustrative discussions above,however, are not intended to be exhaustive or limit the present systemsand methods to the precise forms discussed. Many modifications andvariations are possible in view of the above teachings. The embodimentswere chosen and described in order to explain the principles of thepresent systems and methods and their practical applications, to enableothers skilled in the art to utilize the present systems, apparatus, andmethods and various embodiments with various modifications as may besuited to the particular use contemplated.

What is claimed is:
 1. A DNA sequencing device, comprising: a substrate;a nanochannel extending through a portion of the substrate, thenanochannel having a width in the range of about 0.3 nm to about 20 nm;a pair of in-plane electrodes positioned in the substrate and arrangedsubstantially perpendicular to the nanochannel, a portion of eachelectrode being exposed in the nanochannel to form an electrode gap, theelectrode gap being in the range of about 0.3 nm to about 2 nm.
 2. Thedevice of claim 1, wherein a height of the nanochannel is in the rangeof about 5 nm to about 20 nm.
 3. The device of claim 1, wherein theelectrodes have a width in the range of about 0.1 nm to about 20 nm. 4.The device of claim 1, wherein the electrodes have a height in the rangeof about 5 nm to about 20 nm.
 5. The device of claim 1, wherein thesubstrate is an insulator substrate.
 6. The device of claim 1, furthercomprising a metal layer disposed along a bottom surface of the channeland an insulator material disposed over the metal layer.
 7. The deviceof claim 1, wherein the substrate comprises SiO2 or glass.
 8. The deviceof claim 1, further comprising an actuator associated with a firstelectrode of the pair of electrodes, the actuator configured to displacethe first electrode relative to a second electrode of the pair ofelectrodes.
 9. A method of forming a nanochannel device for DNAsequencing, the method comprising: depositing a hard mask layer on aninsulator substrate; depositing a first resist layer on the hard masklayer; trench patterning the first resist layer to form a first trench;shrinking the first trench using a thermal re-flow process; patterntransferring the first trench through the hard mask layer and into theinsulator substrate; stripping the hard mask layer from the insulatorsubstrate; filling the first trench with a fill material; trenchpatterning the insulator substrate to form an electrode trench, theelectrode trench intersecting the first trench; depositing metalmaterial in the electrode trench to form a pair of electrodes; removingthe fill material from the first trench to form a DNA nanochannel. 10.The method of claim 9, further comprising trench patterning using atleast one of deep ultraviolet (DUV) lithography, 193 nm lithography,e-beam lithography, and nanoimprint lithography (NIL).
 11. The method ofclaim 9, further comprising repeating the step of shrinking the firsttrench until the first trench has a first trench width in the range ofabout 0.3 nm to about 20 nm.
 12. The method of claim 9, whereinshrinking the first trench using a thermal re-flow process includes:disposing a top coat over at least a portion of the substrate and withinthe first trench; baking the device with the top coat at a temperatureof approximately 100° C. to approximately 180° C. for approximately 60seconds to approximately 90 seconds; and removing the top coat from thesubstrate and the first trench.
 13. The method of claim 9, furthercomprising, after stripping the hard mask layer: depositing a metallayer on the insulator substrate as a capping layer, the metal layerpositioned along a bottom surface of the first trench; etching to removethe metal layer from the insulator substrate except in the first trench;depositing an insulator material in the first trench to cover the metallayer deposited in the first trench.
 14. The method of claim 9, whereinfilling the first trench with the filler material comprises: spincoating the filler material on the insulator substrate and in the firsttrench; etching back the filler material from the insulator substrateexcept within the first trench.
 15. The method of claim 9, furthercomprising, after filling the first trench with the filler material:depositing a second resist layer on the insulator substrate; trenchpatterning the second resist layer to form a second trench; shrinkingthe second trench using the thermal re-flow process; trench patterningthe insulator substrate to form the electrode trench using the secondtrench as a pattern.
 16. The method of claim 9, further comprising,after depositing metal material in the electrode trench, etching backthe metal material to expose the fill material.
 17. The method of claim9, wherein the electrodes are spaced apart to form an electrode gap, theelectrode gap positioned in the nanochannel and exhibiting a width inthe range of about 0.3 nm to about 2 nm.
 18. The method of claim 17,further comprising forming at least a first electrode of the electrodepair as a suspended electrode and coupling the first electrode with anactuator to displace the first electrode relative to a second electrodeof the electrode pair to vary the width of the electrode gap.
 19. Themethod of claim 9, wherein a width of nanochannel is in the range ofabout 0.3 nm to about 20 nm, and a height of the nanochannel is in therange of about 5 nm to about 20 nm, and the electrode has a width in therange of about 0.1 nm to about 20 nm, and a height in the range of about5 nm to about 20 nm.
 20. A method of sequencing DNA, comprising:providing a DNA sequencing device having a substrate, a nanochannelextending through a portion of the substrate, the nanochannel having awidth in the range of about 0.3 nm to about 20 nm, and a pair ofin-plane electrodes positioned in the substrate and arrangedsubstantially perpendicular to the nanochannel, a portion of eachelectrode being exposed in the nanochannel to form an electrode gap, theelectrode gap being in the range of about 0.3 nm to about 2 nm; passinga DNA strand through the electrode gap; detecting a change in electronicsignal with the electrodes as the DNA strand passes through theelectrode gap; determining a sequence of individual nucleotides of theDNA strand based on the change in electronic signal.